What is the output of MuTect and how should I interpret it?
Please note that this article refers to the original standalone version of MuTect. A new version is now available within GATK (starting at GATK 3.5) under the name MuTect2. This new version is able to...
View ArticleDo strand flips in the dbSNP or training file cause problems for BQSR, Mutect...
Our group is working on putting together a file of known germline variants in a non-model organism. While we have a large set of known variants, my colleague has noted that some number of these are...
View ArticleGATK haplotype caller: discrepancy between AD and GT
Hi We have come across a few calls as below, where the winning PL and genotype point to 0/1, yet the AD shows zero reads supporting the ALT allele. Is this expected, or is it a bug? chr1 726136 . TGGAA...
View ArticleLow novel Ti/Tv ratio in expanded exome data
Hey! I'm using VSQR to filter variants from expanded exome data including exome (RocheNimblegen v3, 64Mb), HLA region (Roche Nimblegen HLA, 5 Mb) and selection of regulatory regions (64 Mb) captured...
View ArticleDocumentation error in RNAseq workflow
We discovered today that we made an error in the documentation article that describes the RNAseq Best Practices workflow. The error is not critical but is likely to cause an increased rate of False...
View ArticleMuTect Parameter Settings for stringent criteria
I would like to get mutation list with very stringent criteria. Could any one please tell me which parameters I could change, and what value I could set them? Thanks a lot.
View ArticleHow can I exclude snp sites with ALT asterisk by SelectVariants ?
Hello , I am using the latest GATK 3.6 to analysis my human WGS data. For snp analysis, when I ran VariantRecalibrator , it reported error as following: 1 788419 . A * 854.77 PASS DP=33 GT 0/1...
View ArticleGATK best practices somatic mutations
Hi, I would like to know because in the actual best practices there is not the possibility to perform the analysis of the somatic mutations with RNA seq using STAR and mutect. Thank you. Riccardo
View ArticleHard filtering MuTect output based on AD/AF?
I know that MuTect uses a statistical approach to filtering instead of hard coding the filters but I was wondering whether it is still appropriate to use some final hard filters on the call set? For...
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DiagnoseTargets report no reads, but it actually have tons of read. Why?
Hi Sheila, Last time I asked question in this thread http://gatkforums.broadinstitute.org/gatk/discussion/comment/32523#Comment_32523 Then I figured out that I didn't use the correct interval file....
View ArticleIs there a way to disable interval merging in DepthOfCoverage?
Hi All, I'm interested in looking at mean coverage and % bases statistics at all exons of all transcripts. The interval file is prepared with all exonic coordinates (of course, there will be overlap)...
View ArticleTrying to locate SomaticAnalysisTK.jar
Hi, I'm currently working with a Bina box to do tumor-normal whole genome calling, which relies on GATK and related tools to execute. The pipeline always crashes in the middle due to the fact that it...
View ArticlecatVariants in newer versions and gz files
Hi, When I try to run catVariants on a newer version than 2.7.2 I get an error: Error: Could not find or load main class org.broadinstitute.sting.tools.CatVariants The following code works perfectly...
View ArticleException counting mismatches for read...
I am trying to merge a aligned bam file with unaligned barcod bam, but I am getting this error: [Thu Sep 08 09:14:37 CEST 2016] picard.sam.MergeBamAlignment done. Elapsed time: 34.03 minutes....
View ArticleRunning MuTect2 with Stringent Criteria
There are many parameters we can change, but which parameters are most critical? I would like to get somatic mutation list with much confidence. Which parameter would you recommend me to change and...
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Soliciting developer feedback on plans to merge Picard + GATK4
Cross-posted from https://github.com/broadinstitute/picard/issues/647 For many years now we’ve been hearing from users of both GATK and Picard about how they’d love to see the two projects unite into a...
View ArticleAF calculation in Mutect2
Hi, I've been calling somatic mutations with Mutect2, and have noted that the AF calculation does not always correlate to DP alt/(DP ref+DP alt). For example, consider this indel: T057.mutect2.vcf:7...
View ArticleConfused about Bootstrapping a set of known sites for Base Recalibration
Dear all, I am working on genomic data from a non-human organism (nematode) for which I do not have a set of known variant sites. The aim of my study is to find the variants within and between 2...
View ArticleMutect2 --ignore-soft-clip-bases
Hello, We are running Mutect2 with the option to ignore soft clipped bases. This has significantly reduced our false positives, but the ALT and REF counts from the remaining reads do not seem to...
View ArticleWhat should I use as known variants/sites for running tool X?
1. Notes on known sites Why are they important? Each tool uses known sites differently, but what is common to all is that they use them to help distinguish true variants from false positives, which is...
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